Lab members:

The ultimate goal of this project is to develop eco-friendly economically sustainable bioenergy crops in the future by decreasing their dependency on fertilizer use.

Nitrogen (N) is an essential component of DNA and proteins and consequently, a key element for life and cell development. Mineral N is often limited in plants, which negatively affects plant growth and hence biomass yields. In natural ecosystems, microbes play a fundamental role in producing bioavailable N for plants. The plant rhizosphere, for example, contains diazotrophic (N-fixing) bacteria without the requirement of forming mutualistic association with a plant host. Recently, diazotrophic endophytic bacteria colonizing roots, stems and leaves in several non-legume plants, have been identified. To better understand and optimize interactions between bioenergy crops and diazotrophic endophytes, my project incorporates a two-tiered scientific approach: identification and isolation of diazotrophic endophytes as well as discovery of new principles and molecular mechanisms in plant-microbe interactions.

2013- now Postdoctoral Fellow in the Chakraborty laboratory at Lawrence Berkeley National Laboratory (USA).

10-2009 to 7-2012: PhD Student in Microbiology in the Gescher laboratory at Karlsruhe Institute of Technology (Germany)

7-2008 to 9-2008: Visiting Student Researcher in the Spormann laboratory at Stanford University (USA)

10-2004 to 7-2008: Diploma Student in Biochemistry and Microbiology in the Gescher laboratory at Albert-Ludwigs-University Freiburg i. Br. (Germany)

Angelica Pettenato (Research Assistant)Angelica Pettenato has been working as a research assistant under Romy Chakraborty since 2011. She currently works on characterization of anaerobic environmental microbes from Oakridge FRC as part of the ENIGMA project and Alaskan permafrost as a part of the Next-Generation Ecosystem Experiments (NGEE) project. Her previous projects in the lab has included oil bioremediation in the Gulf of Mexico and bacteria-algae interactions in Northern California’s Eel River. She began working at Berkeley Lab in 2010 while studying Environmental Earth Science at UC Berkeley.

Bryson Cwick (Student Research Assistant)I work primarily on the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) project. I work to isolate aerobic and anaerobic bacteria for DNA extraction and sequencing. I also have worked on peatland project (Indonesia), involving methane respiring bacteria.

September 2011 to present: Undergraduate student at University Of California, Berkeley studying Molecular and Cell Biology: Neuroscience.

June to August 2012: Internship under Dr. Winter at the Alpine Orthopedic Medical Center, Surgery Center, and Dameron Hospital.

September 2013 to present: Research Assistant in the Chakraborty Lab at the Lawrence Berkeley National Lab.

Undergraduate Research Interns:

Rattanah Mahal

Rattanah Mahal is working with Postdoc in the group Marcus Schicklberger to isolate N-fixing and P-solubilizing bacteria from different plant roots and shoots.

Husna Yasini

Husna Yasini is working to isolate and characterize microbes from few contaminated groundwater wells at DOE-FRC site in Oakridge, TN. These specific wells are high in nitrate and low in pH (3).

Jeanine Porzio

I am an intern in the Chakraborty lab through the Cal Energy Corps program and I work on the project studying plant-microbe interactions with Dr. Marcus Schicklberger. I study how the microbiome associated with the roots of the bioenergy crops, tobacco and switchgrass, differs in varying conditions. In particular, I will investigate how the increasing prevalence of drought associated with climate change will affect nitrogen fixation by bacteria and I will study how the microbial community changes during the development of the switchgrass and tobacco.

Visiting Scholars:

Julia Lima Perim

Microbial diversity involved in the nitrogen cycle in soil of sugarcane crops in Brazil

Brazil is the largest sugarcane producer in the world and São Paulo State is responsible for 56% of the total production. Considering crop productivity and sustainability, a better understanding of the microbial composition in these soils, as well as the role that microorganisms involved in the nitrogen (N) cycle play is of utmost importance, since they are responsible for the availability of this element to plants. However, little is known about the microbial community related to this biogeochemical cycle in soil of sugarcane fields and our sample areas, for the first time, offer a range of different management conditions and characteristics. The next generation sequencing approach allows detect organisms that exist in very low abundance within complex populations and, as a result, the ability to detect low abundance populations can profoundly impact the interpretation of microbiological changes, allowing full view of the composition of the N cycle communities that are extremely important to soil system. The NGS data will provide the basis for multivariate analysis, linking them with other data already obtained within the PhD project.